LAMMPS (27 Nov 2018)
  using 1 OpenMP thread(s) per MPI task
# sample surface deposition script for molecules

units		lj
atom_style      bond
boundary        p p f

lattice		fcc 1.0
Lattice spacing in x,y,z = 1.5874 1.5874 1.5874
region          box block 0 5 0 5 0 10
create_box      3 box bond/types 1 extra/bond/per/atom 1
Created orthogonal box = (0 0 0) to (7.93701 7.93701 15.874)
  1 by 1 by 4 MPI processor grid

region		substrate block INF INF INF INF INF 3
create_atoms	1 region substrate
Created 350 atoms
  Time spent = 0.000810623 secs

pair_style	lj/cut 2.5
pair_coeff	* * 1.0 1.0
pair_coeff	1 2 1.0 1.0 5.0
mass		* 1.0

bond_style	harmonic
bond_coeff      1 5.0 1.0

neigh_modify	delay 0

group		addatoms type 2
0 atoms in group addatoms
region          mobile block 0 5 0 5 2 INF
group		mobile region mobile
150 atoms in group mobile

compute		add addatoms temp
compute_modify	add dynamic/dof yes extra/dof 0

fix		1 addatoms nve
fix		2 mobile langevin 0.1 0.1 0.1 587283
fix		3 mobile nve

molecule        dimer molecule.dimer.shake
Read molecule dimer:
  2 atoms with max type 3
  1 bonds with max type 1
  0 angles with max type 0
  0 dihedrals with max type 0
  0 impropers with max type 0
region          slab block 0 5 0 5 8 9
fix		4 addatoms deposit 100 0 100 12345 region slab near 1.0                 mol dimer vz -1.0 -1.0 shake 6
fix		5 addatoms wall/reflect zhi EDGE
fix             6 all shake 0.0001 20 1000 b 1 mol dimer
  0 = # of size 2 clusters
  0 = # of size 3 clusters
  0 = # of size 4 clusters
  0 = # of frozen angles

thermo_style	custom step atoms temp epair etotal press
thermo          100
thermo_modify	temp add lost/bond ignore lost warn
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488)

#dump		1 all atom 50 dump.deposit.atom

#dump		2 all image 50 image.*.jpg type type #		axes yes 0.8 0.02 view 80 -30
#dump_modify	2 pad 5

#dump		3 all movie 50 tmp.mpg type type #		axes yes 0.8 0.02 view 80 -30
#dump_modify	3 pad 5

run             10000
Neighbor list info ...
  update every 1 steps, delay 0 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 5.3
  ghost atom cutoff = 5.3
  binsize = 2.65, bins = 3 3 6
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/cut, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d/newton
      bin: standard
SHAKE stats (type/ave/delta) on step 0
Per MPI rank memory allocation (min/avg/max) = 0.4411 | 3.816 | 5.101 Mbytes
Step Atoms Temp E_pair TotEng Press 
       0      350            0   -6.9215833   -6.9215833   -1.0052629 
     100      352    1.0079368   -6.8946578   -6.8874992  -0.73775337 
     200      354    1.0079368   -6.8644786   -6.8502422  -0.69623155 
     300      356    1.0098741   -6.8219324    -6.800657  -0.69552497 
     400      358     1.015821    -6.775427   -6.7470521  -0.67240912 
     500      360    1.0431742   -6.7311558   -6.6949345  -0.69505765 
     600      362    1.0978772   -6.7107816   -6.6652895  -0.66124338 
     700      364    1.0536993   -6.6818292   -6.6311706  -0.67789771 
     800      366    1.0615655   -6.6354474   -6.5774383  -0.64710621 
     900      368    1.1688557    -6.614281   -6.5428156  -0.64842218 
SHAKE stats (type/ave/delta) on step 1000
  1 1 1.22125e-15
    1000      370    1.2172009   -6.5772424   -6.4949991  -0.67942188 
    1100      372    1.1031034     -6.55895   -6.4774034  -0.65896897 
    1200      374     1.040192   -6.5874108    -6.503973  -0.62919433 
    1300      376   0.94890463   -6.5897148   -6.5076952  -0.63346087 
    1400      378   0.78945672   -6.5952649    -6.522167  -0.67613271 
    1500      380   0.82876461   -6.5798609   -6.4980749  -0.65306056 
    1600      382   0.73883758   -6.5591084   -6.4817432  -0.62749488 
    1700      384   0.73539709   -6.5556021   -6.4742105  -0.66817567 
    1800      386   0.67455206   -6.5535874    -6.474948  -0.57721026 
    1900      388   0.66352723   -6.5469905   -6.4657597  -0.69276627 
SHAKE stats (type/ave/delta) on step 2000
  1 1 2.22045e-15
    2000      390   0.81013116   -6.5567994   -6.4529364  -0.71579948 
    2100      392   0.72889872   -6.5689128   -6.4712924  -0.65504494 
    2200      394   0.57901901    -6.552299   -6.4714715  -0.67723953 
    2300      396   0.59157803   -6.5485081   -6.4626098  -0.66397554 
    2400      398   0.70712699   -6.5593644   -6.4527623  -0.70641253 
    2500      400    0.7569242    -6.576119   -6.4578496  -0.69907756 
    2600      402    0.6662505   -6.6038869   -6.4961599  -0.66941055 
    2700      404   0.51455113   -6.6038412   -6.5178704  -0.69578494 
    2800      406   0.58401979   -6.6058664   -6.5051733  -0.70647457 
    2900      408   0.50129416   -6.6138934   -6.5248154  -0.64390758 
SHAKE stats (type/ave/delta) on step 3000
  1 1 2.66454e-15
    3000      410   0.44807689   -6.6222658   -6.5403005  -0.68340233 
    3100      412   0.45962393   -6.6204312   -6.5339728  -0.66309459 
    3200      414   0.50182826   -6.6295842   -6.5326126  -0.74122586 
    3300      416   0.48471205   -6.6424495   -6.5463227  -0.69764601 
    3400      418   0.36856546   -6.6251783   -6.5502308  -0.76543921 
    3500      420    0.4203509   -6.6198957   -6.5323226  -0.64154608 
    3600      422   0.54795097   -6.6410801   -6.5242185   -0.7463818 
    3700      424   0.51183952   -6.6521145   -6.5404514  -0.70304908 
    3800      426   0.39414561   -6.6456807   -6.5577844  -0.74178922 
    3900      428   0.40589341   -6.6564647   -6.5640007  -0.78327027 
SHAKE stats (type/ave/delta) on step 4000
  1 1 1.88738e-15
    4000      430   0.43166847   -6.6566443   -6.5562563  -0.73290988 
    4100      432   0.40408931   -6.6500622   -6.5541845  -0.73057986 
    4200      434   0.35377187   -6.6356255   -6.5500355  -0.76557381 
    4300      436    0.4291929    -6.657321   -6.5514993  -0.78608144 
    4400      438   0.43151668   -6.6494979   -6.5411262  -0.70820395 
    4500      440   0.44315446   -6.6596739   -6.5463674  -0.82000058 
    4600      442   0.41285261   -6.6553044    -6.547888  -0.76115447 
    4700      444   0.38354616   -6.6502515     -6.54875   -0.6954286 
    4800      446   0.39108666    -6.648355   -6.5431299  -0.72779836 
    4900      448    0.3799768   -6.6517925   -6.5478926  -0.79771549 
SHAKE stats (type/ave/delta) on step 5000
  1 1 3.10862e-15
    5000      450   0.39260452   -6.6598567   -6.5507999  -0.76677324 
    5100      452   0.41475009   -6.6627963   -6.5458038  -0.70468384 
    5200      454    0.4115583   -6.6658575   -6.5480104  -0.78115993 
    5300      456    0.3753641   -6.6631393   -6.5540696  -0.78711192 
    5400      458   0.36565536   -6.6545908   -6.5468103  -0.74549556 
    5500      460   0.33271655   -6.6418893    -6.542436  -0.76780862 
    5600      462   0.36832168   -6.6440805   -6.5324679  -0.75143503 
    5700      464   0.39059076   -6.6481163   -6.5281612  -0.78380485 
    5800      466   0.36650802   -6.6430337   -6.5289916  -0.75502025 
    5900      468   0.35914314   -6.6418801   -6.5286886  -0.67704807 
SHAKE stats (type/ave/delta) on step 6000
  1 1 2.22045e-15
    6000      470   0.39116517   -6.6612874   -6.5364474  -0.84800605 
    6100      472   0.38421704   -6.6693489    -6.545211  -0.78734456 
    6200      474   0.38216918   -6.6812774   -6.5563065  -0.81814647 
    6300      476   0.34722048   -6.6730701   -6.5581809  -0.77616674 
    6400      478   0.32907391   -6.6719973   -6.5618471   -0.7458085 
    6500      480   0.31094699   -6.6715976    -6.566329  -0.83282406 
    6600      482   0.35169592   -6.6680323   -6.5476384  -0.85138473 
    6700      484   0.36350925   -6.6706468   -6.5448456  -0.71970784 
    6800      486   0.38133383   -6.6922722   -6.5588839  -0.77339402 
    6900      488   0.34810579   -6.6746177    -6.551568  -0.77360649 
SHAKE stats (type/ave/delta) on step 7000
  1 1 3.66374e-15
    7000      490    0.3590117    -6.683101   -6.5548825  -0.80004574 
    7100      492   0.38269726    -6.688913   -6.5508464  -0.81445922 
    7200      494   0.31934554   -6.6944357    -6.578075  -0.74069497 
    7300      496   0.32758627   -6.6955862   -6.5750529  -0.78679117 
    7400      498    0.3660502   -6.7111626   -6.5751801  -0.78104263 
    7500      500   0.32569889   -6.6953555   -6.5732185  -0.74496853 
    7600      502   0.33737271   -6.6971694   -6.5694785  -0.90240288 
    7700      504   0.35222518   -6.7006509   -6.5661204  -0.86220892 
    7800      506   0.31834385   -6.6988433   -6.5761614  -0.78723443 
    7900      508   0.35977076   -6.7264843   -6.5866128   -0.8568963 
SHAKE stats (type/ave/delta) on step 8000
  1 1 2.22045e-15
    8000      510   0.35931856   -6.7266146   -6.5857054  -0.85544232 
    8100      512   0.36797798    -6.739034   -6.5934958  -0.82062699 
    8200      514   0.40277035   -6.7571847   -6.5965467  -0.82121365 
    8300      516   0.32568144   -6.7419653   -6.6109984  -0.78580816 
    8400      518   0.33705466   -6.7532799   -6.6166361  -0.83332745 
    8500      520   0.30158673   -6.7342587   -6.6110142   -0.8578352 
    8600      522   0.32525112   -6.7446972   -6.6107336     -0.96759 
    8700      524   0.32985772   -6.7480971    -6.611181  -0.78464535 
    8800      526   0.32397396   -6.7465569   -6.6110545  -0.81041129 
    8900      528   0.33669589   -6.7543874   -6.6125032  -0.87866197 
SHAKE stats (type/ave/delta) on step 9000
  1 1 3.88578e-15
    9000      530   0.32538398   -6.7436298   -6.6054951  -0.79985713 
    9100      532    0.3336509   -6.7541485   -6.6114688  -0.84449566 
    9200      534   0.31516122   -6.7553334   -6.6195898  -0.88997909 
    9300      536   0.30963064   -6.7627673   -6.6284593  -0.75349544 
    9400      538   0.34228518   -6.7754099   -6.6258988  -0.77001741 
    9500      540   0.29032769   -6.7737667   -6.6460763  -0.85854407 
    9600      542   0.31033087   -6.7764458     -6.63903   -0.8553105 
    9700      544   0.33657054   -6.7798228    -6.629789  -0.91356823 
    9800      546   0.30235172   -6.7634263   -6.6277557  -0.92787364 
    9900      548    0.3446797   -6.7794717   -6.6237998  -0.88766558 
SHAKE stats (type/ave/delta) on step 10000
  1 1 2.55351e-15
   10000      550   0.30296128   -6.7756768   -6.6379672  -0.84420968 
Loop time of 6.71355 on 4 procs for 10000 steps with 550 atoms

Performance: 643474.692 tau/day, 1489.525 timesteps/s
95.0% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.0023715  | 1.0684     | 3.1403     | 123.9 | 15.91
Bond    | 0.0018587  | 0.0045958  | 0.011149   |   5.6 |  0.07
Neigh   | 0.0059454  | 0.74298    | 2.4218     | 114.9 | 11.07
Comm    | 0.53191    | 3.1926     | 5.7443     | 113.9 | 47.55
Output  | 0.0028977  | 0.0060919  | 0.010627   |   4.2 |  0.09
Modify  | 0.47242    | 1.5021     | 4.1679     | 126.1 | 22.37
Other   |            | 0.1969     |            |       |  2.93

Nlocal:    137.5 ave 300 max 2 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Nghost:    1874.5 ave 2648 max 509 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Neighs:    9185.75 ave 23231 max 0 min
Histogram: 2 0 0 0 0 1 0 0 0 1

Total # of neighbors = 36743
Ave neighs/atom = 66.8055
Ave special neighs/atom = 0.363636
Neighbor list builds = 833
Dangerous builds = 0
Total wall time: 0:00:06
